How to get rid of the tornadoes?

To protect your villagers and banish tornadoes without tapping on them you should build Defensive Towers. You can find these constructions in the third tab of the Store window (icon with a mallet in the lower part of the screen). Note that this building will become available only on high game levels.
Another way to get rid of tornadoes is to complete relative quests. They will appear according to the storyline so keep playing and advance in the game.